Abstract
BackgroundIn the pig production industry, artificial insemination (AI) plays an important role in enlarging the beneficial impact of elite boars. Understanding the genetic architecture and detecting genetic markers associated with semen traits can help in improving genetic selection for such traits and accelerate genetic progress. In this study, we utilized a weighted single-step genome-wide association study (wssGWAS) procedure to detect genetic regions and further candidate genes associated with semen traits in a Duroc boar population. Overall, the full pedigree consists of 5284 pigs (12 generations), of which 2693 boars have semen data (143,113 ejaculations) and 1733 pigs were genotyped with 50 K single nucleotide polymorphism (SNP) array.ResultsResults show that the most significant genetic regions (0.4 Mb windows) explained approximately 2%~ 6% of the total genetic variances for the studied traits. Totally, the identified significant windows (windows explaining more than 1% of total genetic variances) explained 28.29, 35.31, 41.98, and 20.60% of genetic variances (not phenotypic variance) for number of sperm cells, sperm motility, sperm progressive motility, and total morphological abnormalities, respectively. Several genes that have been previously reported to be associated with mammal spermiogenesis, testes functioning, and male fertility were detected and treated as candidate genes for the traits of interest: Number of sperm cells, TDRD5, QSOX1, BLK, TIMP3, THRA, CSF3, and ZPBP1; Sperm motility, PPP2R2B, NEK2, NDRG, ADAM7, SKP2, and RNASET2; Sperm progressive motility, SH2B1, BLK, LAMB1, VPS4A, SPAG9, LCN2, and DNM1; Total morphological abnormalities, GHR, SELENOP, SLC16A5, SLC9A3R1, and DNAI2.ConclusionsIn conclusion, candidate genes associated with Duroc boars’ semen traits, including the number of sperm cells, sperm motility, sperm progressive motility, and total morphological abnormalities, were identified using wssGWAS. KEGG and GO enrichment analysis indicate that the identified candidate genes were enriched in biological processes and functional terms may be involved into spermiogenesis, testes functioning, and male fertility.
Highlights
In the pig production industry, artificial insemination (AI) plays an important role in enlarging the beneficial impact of elite boars
In this study, we identified genomic regions associated with semen traits in a Duroc boar population via weighted single-step genome-wide association study (wssGWAS) [6]
In order to investigate the genetic background of the semen traits under consideration, we estimated the heritabilities of these traits by fitting model (1) using the pedigree derived numerator relationship matrix
Summary
In the pig production industry, artificial insemination (AI) plays an important role in enlarging the beneficial impact of elite boars. We utilized a weighted single-step genome-wide association study (wssGWAS) procedure to detect genetic regions and further candidate genes associated with semen traits in a Duroc boar population. With the fast development of sequencing technology and commercially availability of dense marker panels, researchers can precisely identify quantitative trait loci (QTL) by searching for association between genetic markers and phenotypic records, which is known as genome-wide association study (GWAS) [4] Though many challenges, such as the need for efficient study design especially for replication efforts and technologies for capturing genetic variation, the missing heritability problem, reducing the bias introduced into a dataset, and utilizing of new resources available, remained to be addressed [5], GWAS has been successfully implemented in detecting genetic risk factors for human diseases and mapping QTL for economically important traits in both animal and plant breeding populations. Genetic variance of certain chromosome window is subsequently calculated as the variation of the genetic values possessed by SNPs located in that window (i.e., Var(Zwindowgwindow), Zwindow and gwindow represent genotypes and marker effects of SNPs located in the window, respectively)
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